A marine vessel running controlling apparatus is applicable to a marine vessel which includes a propulsive force generating unit arranged to generate a propulsive force to be applied to a hull of the marine vessel, and a steering unit arranged to turn the hull. The marine vessel running controlling apparatus includes an operational unit to be operated by an operator of the marine vessel to control a steering angle of the steering unit, and a control unit arranged to update control information related to the steering angle of the steering unit with respect to an operation amount of the operational unit based on data acquired during travel of the marine vessel.